7W9R

Crystal structure of V30M-TTR in complex with naringenin derivative-18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Chlorinated Naringenin Analogues as Potential Inhibitors of Transthyretin Amyloidogenesis.

Mizuguchi, M.Nakagawa, Y.Inui, K.Katayama, W.Sawai, Y.Shimane, A.Kitakami, R.Okada, T.Nabeshima, Y.Yokoyama, T.Kanamitsu, K.Nakagawa, S.Toyooka, N.

(2022) J Med Chem 65: 16218-16233

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00511
  • Primary Citation of Related Structures:  
    7W9Q, 7W9R

  • PubMed Abstract: 

    Misfolding and aggregation of transthyretin are implicated in the fatal systemic disease known as transthyretin amyloidosis. Here, we report the development of a naringenin derivative bearing two chlorine atoms that will be efficacious for preventing aggregation of transthyretin in the eye. The amyloid inhibitory activity of the naringenin derivative was as strong as that of tafamidis, which is the first therapeutic agent targeting transthyretin in the plasma. X-ray crystal structures of the compounds in complex with transthyretin demonstrated that the naringenin derivative with one chlorine bound to the thyroxine-binding site of transthyretin in the forward mode and that the derivative with two chlorines bound to it in the reverse mode. An ex vivo competitive binding assay showed that naringenin derivatives exhibited more potent binding than tafamidis in the plasma. Furthermore, an in vivo pharmacokinetic study demonstrated that the dichlorinated derivative was significantly delivered to the eye.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0914, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transthyretin
A, B
159Homo sapiensMutation(s): 1 
Gene Names: TTRPALB
UniProt & NIH Common Fund Data Resources
Find proteins for P02766 (Homo sapiens)
Explore P02766 
Go to UniProtKB:  P02766
PHAROS:  P02766
GTEx:  ENSG00000118271 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02766
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
91C (Subject of Investigation/LOI)
Query on 91C

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2~{R})-2-[3,5-bis(chloranyl)-4-oxidanyl-phenyl]-5,7-bis(oxidanyl)-2,3-dihydrochromen-4-one
C15 H10 Cl2 O5
QMQREYZMFZIOBC-GFCCVEGCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.766α = 90
b = 84.477β = 90
c = 64.071γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description